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- EMDB-20233: Q21 transcription antitermination complex: loading complex -

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Basic information

Entry
Database: EMDB / ID: EMD-20233
TitleQ21 transcription antitermination complex: loading complex
Map dataQ21 transcription antitermination complex: loading complex
Sample
  • Complex: Q21-loading complex
    • DNA: x 2 types
    • Protein or peptide: x 6 types
    • RNA: x 1 types
  • Ligand: x 2 types
KeywordsRNA polymerase / DNA Binding / transcription / Q-dependent antitermination / Q antiterminator factor / GENE REGULATION
Function / homology
Function and homology information


negative regulation of termination of DNA-templated transcription / sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex ...negative regulation of termination of DNA-templated transcription / sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / cell motility / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / negative regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Bacteriophage 933W, GpQ / Phage antitermination protein Q / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD ...Bacteriophage 933W, GpQ / Phage antitermination protein Q / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
RNA polymerase sigma factor RpoD / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / Q protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Phage 21 (virus) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYin Z / Ebright RH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)GM041376 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Structural basis of Q-dependent antitermination.
Authors: Zhou Yin / Jason T Kaelber / Richard H Ebright /
Abstract: Lambdoid bacteriophage Q protein mediates the switch from middle to late bacteriophage gene expression by enabling RNA polymerase (RNAP) to read through transcription terminators preceding ...Lambdoid bacteriophage Q protein mediates the switch from middle to late bacteriophage gene expression by enabling RNA polymerase (RNAP) to read through transcription terminators preceding bacteriophage late genes. Q loads onto RNAP engaged in promoter-proximal pausing at a Q binding element (QBE) and adjacent sigma-dependent pause element (SDPE) to yield a Q-loading complex, and Q subsequently translocates with RNAP as a pausing-deficient, termination-deficient Q-loaded complex. Here, we report high-resolution structures of 4 states on the pathway of antitermination by Q from bacteriophage 21 (Q21): Q21, the Q21-QBE complex, the Q21-loading complex, and the Q21-loaded complex. The results show that Q21 forms a torus, a "nozzle," that narrows and extends the RNAP RNA-exit channel, extruding topologically linked single-stranded RNA and preventing the formation of pause and terminator hairpins.
History
DepositionMay 19, 2019-
Header (metadata) releaseJun 12, 2019-
Map releaseJun 26, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0286
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0286
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6p18
  • Surface level: 0.0286
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20233.png

Downloads & links

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Map

FileDownload / File: emd_20233.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationQ21 transcription antitermination complex: loading complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 272.896 Å		1.07 Å/pix.
x 256 pix.
= 272.896 Å		1.07 Å/pix.
x 256 pix.
= 272.896 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.066 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0286 / Movie #1: 0.0286
Minimum - Maximum-0.20461327 - 0.32438824
Average (Standard dev.)-0.00005341659 (±0.008255954)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 272.896 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0661.0661.066
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z272.896272.896272.896
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ304304304
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.2050.324-0.000

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Supplemental data

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Sample components

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Entire : Q21-loading complex

EntireName: Q21-loading complex
Components
  • Complex: Q21-loading complex
    • DNA: DNA (67-MER) fragment carrying phage-21 pR' promoter and pause element, nontemplate strand
    • DNA: DNA (67-MER) fragment carrying phage-21 pR' promoter and pause element, template strand
    • Protein or peptide: DNA-directed RNA polymerase subunit alpha
    • Protein or peptide: DNA-directed RNA polymerase subunit beta
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'
    • Protein or peptide: DNA-directed RNA polymerase subunit omega
    • Protein or peptide: RNA polymerase sigma factor RpoD
    • Protein or peptide: Q protein
    • RNA: RNA (5'-R(P*UP*GP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Q21-loading complex

SupramoleculeName: Q21-loading complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: DNA (67-MER) fragment carrying phage-21 pR' promoter and pause el...

MacromoleculeName: DNA (67-MER) fragment carrying phage-21 pR' promoter and pause element, nontemplate strand
type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Phage 21 (virus)
Molecular weightTheoretical: 20.704312 KDa
SequenceString: (DT)(DG)(DA)(DC)(DA)(DT)(DC)(DA)(DT)(DT) (DG)(DA)(DG)(DC)(DA)(DA)(DA)(DT)(DG)(DA) (DG)(DC)(DA)(DA)(DC)(DA)(DC)(DT)(DA) (DT)(DT)(DC)(DG)(DC)(DA)(DT)(DA)(DT)(DA) (DA) (DT)(DG)(DG)(DG)(DG)(DT) ...String:
(DT)(DG)(DA)(DC)(DA)(DT)(DC)(DA)(DT)(DT) (DG)(DA)(DG)(DC)(DA)(DA)(DA)(DT)(DG)(DA) (DG)(DC)(DA)(DA)(DC)(DA)(DC)(DT)(DA) (DT)(DT)(DC)(DG)(DC)(DA)(DT)(DA)(DT)(DA) (DA) (DT)(DG)(DG)(DG)(DG)(DT)(DT)(DA) (DG)(DT)(DG)(DA)(DC)(DT)(DC)(DT)(DT)(DA) (DA)(DG) (DT)(DT)(DG)(DC)(DA)(DA)(DC)

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Macromolecule #2: DNA (67-MER) fragment carrying phage-21 pR' promoter and pause el...

MacromoleculeName: DNA (67-MER) fragment carrying phage-21 pR' promoter and pause element, template strand
type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Phage 21 (virus)
Molecular weightTheoretical: 20.588207 KDa
SequenceString: (DG)(DT)(DT)(DG)(DC)(DA)(DA)(DC)(DT)(DT) (DA)(DA)(DG)(DA)(DG)(DT)(DC)(DA)(DT)(DT) (DA)(DC)(DC)(DT)(DC)(DT)(DC)(DC)(DA) (DT)(DA)(DA)(DT)(DG)(DC)(DG)(DA)(DA)(DT) (DA) (DG)(DT)(DG)(DT)(DT)(DG) ...String:
(DG)(DT)(DT)(DG)(DC)(DA)(DA)(DC)(DT)(DT) (DA)(DA)(DG)(DA)(DG)(DT)(DC)(DA)(DT)(DT) (DA)(DC)(DC)(DT)(DC)(DT)(DC)(DC)(DA) (DT)(DA)(DA)(DT)(DG)(DC)(DG)(DA)(DA)(DT) (DA) (DG)(DT)(DG)(DT)(DT)(DG)(DC)(DT) (DC)(DA)(DT)(DT)(DT)(DG)(DC)(DT)(DC)(DA) (DA)(DT) (DG)(DA)(DT)(DG)(DT)(DC)(DA)

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Macromolecule #3: DNA-directed RNA polymerase subunit alpha

MacromoleculeName: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 36.55868 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MQGSVTEFLK PRLVDIEQVS STHAKVTLEP LERGFGHTLG NALRRILLSS MPGCAVTEVE IDGVLHEYST KEGVQEDILE ILLNLKGLA VRVQGKDEVI LTLNKSGIGP VTAADITHDG DVEIVKPQHV ICHLTDENAS ISMRIKVQRG RGYVPASTRI H SEEDERPI ...String:
MQGSVTEFLK PRLVDIEQVS STHAKVTLEP LERGFGHTLG NALRRILLSS MPGCAVTEVE IDGVLHEYST KEGVQEDILE ILLNLKGLA VRVQGKDEVI LTLNKSGIGP VTAADITHDG DVEIVKPQHV ICHLTDENAS ISMRIKVQRG RGYVPASTRI H SEEDERPI GRLLVDACYS PVERIAYNVE AARVEQRTDL DKLVIEMETN GTIDPEEAIR RAATILAEQL EAFVDLRDVR QP EVKEEKP EFDPILLRPV DDLELTVRSA NCLKAEAIHY IGDLVQRTEV ELLKTPNLGK KSLTEIKDVL ASRGLSLGMR LEN WPPASI ADE

UniProtKB: DNA-directed RNA polymerase subunit alpha

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Macromolecule #4: DNA-directed RNA polymerase subunit beta

MacromoleculeName: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 150.820875 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MVYSYTEKKR IRKDFGKRPQ VLDVPYLLSI QLDSFQKFIE QDPEGQYGLE AAFRSVFPIQ SYSGNSELQY VSYRLGEPVF DVQECQIRG VTYSAPLRVK LRLVIYEREA PEGTVKDIKE QEVYMGEIPL MTDNGTFVIN GTERVIVSQL HRSPGVFFDS D KGKTHSSG ...String:
MVYSYTEKKR IRKDFGKRPQ VLDVPYLLSI QLDSFQKFIE QDPEGQYGLE AAFRSVFPIQ SYSGNSELQY VSYRLGEPVF DVQECQIRG VTYSAPLRVK LRLVIYEREA PEGTVKDIKE QEVYMGEIPL MTDNGTFVIN GTERVIVSQL HRSPGVFFDS D KGKTHSSG KVLYNARIIP YRGSWLDFEF DPKDNLFVRI DRRRKLPATI ILRALNYTTE QILDLFFEKV IFEIRDNKLQ ME LVPERLR GETASFDIEA NGKVYVEKGR RITARHIRQL EKDDVKLIEV PVEYIAGKVV AKDYIDESTG ELICAANMEL SLD LLAKLS QSGHKRIETL FTNDLDHGPY ISETLRVDPT NDRLSALVEI YRMMRPGEPP TREAAESLFE NLFFSEDRYD LSAV GRMKF NRSLLREEIE GSGILSKDDI IDVMKKLIDI RNGKGEVDDI DHLGNRRIRS VGEMAENQFR VGLVRVERAV KERLS LGDL DTLMPQDMIN AKPISAAVKE FFGSSQLSQF MDQNNPLSEI THKRRISALG PGGLTRERAG FEVRDVHPTH YGRVCP IET PEGPNIGLIN SLSVYAQTNE YGFLETPYRK VTDGVVTDEI HYLSAIEEGN YVIAQANSNL DEEGHFVEDL VTCRSKG ES SLFSRDQVDY MDVSTQQVVS VGASLIPFLE HDDANRALMG ANMQRQAVPT LRADKPLVGT GMERAVAVDS GVTAVAKR G GVVQYVDASR IVIKVNEDEM YPGEAGIDIY NLTKYTRSNQ NTCINQMPCV SLGEPVERGD VLADGPSTDL GELALGQNM RVAFMPWNGY NFEDSILVSE RVVQEDRFTT IHIQELACVS RDTKLGPEEI TADIPNVGEA ALSKLDESGI VYIGAEVTGG DILVGKVTP KGETQLTPEE KLLRAIFGEK ASDVKDSSLR VPNGVSGTVI DVQVFTRDGV EKDKRALEIE EMQLKQAKKD L SEELQILE AGLFSRIRAV LVAGGVEAEK LDKLPRDRWL ELGLTDEEKQ NQLEQLAEQY DELKHEFEKK LEAKRRKITQ GD DLAPGVL KIVKVYLAVK RRIQPGDKMA GRHGNKGVIS KINPIEDMPY DENGTPVDIV LNPLGVPSRM NIGQILETHL GMA AKGIGD KINAMLKQQQ EVAKLREFIQ RAYDLGADVR QKVDLSTFSD EEVMRLAENL RKGMPIATPV FDGAKEAEIK ELLK LGDLP TSGQIRLYDG RTGEQFERPV TVGYMYMLKL NHLVDDKMHA RSTGSYSLVT QQPLGGKAQF GGQRFGEMEV WALEA YGAA YTLQEMLTVK SDDVNGRTKM YKNIVDGNHQ MEPGMPESFN VLLKEIRSLG INIELEDE

UniProtKB: DNA-directed RNA polymerase subunit beta

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Macromolecule #5: DNA-directed RNA polymerase subunit beta'

MacromoleculeName: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 158.314891 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKDLLKFLKA QTKTEEFDAI KIALASPDMI RSWSFGEVKK PETINYRTFK PERDGLFCAR IFGPVKDYEC LCGKYKRLKH RGVICEKCG VEVTQTKVRR ERMGHIELAS PTAHIWFLKS LPSRIGLLLD MPLRDIERVL YFESYVVIEG GMTNLERQQI L TEEQYLDA ...String:
MKDLLKFLKA QTKTEEFDAI KIALASPDMI RSWSFGEVKK PETINYRTFK PERDGLFCAR IFGPVKDYEC LCGKYKRLKH RGVICEKCG VEVTQTKVRR ERMGHIELAS PTAHIWFLKS LPSRIGLLLD MPLRDIERVL YFESYVVIEG GMTNLERQQI L TEEQYLDA LEEFGDEFDA KMGAEAIQAL LKSMDLEQEC EQLREELNET NSETKRKKLT KRIKLLEAFV QSGNKPEWMI LT VLPVLPP DLRPLVPLDG GRFATSDLND LYRRVINRNN RLKRLLDLAA PDIIVRNEKR MLQEAVDALL DNGRRGRAIT GSN KRPLKS LADMIKGKQG RFRQNLLGKR VDYSGRSVIT VGPYLRLHQC GLPKKMALEL FKPFIYGKLE LRGLATTIKA AKKM VEREE AVVWDILDEV IREHPVLLNR APTLHRLGIQ AFEPVLIEGK AIQLHPLVCA AYNADFDGDQ MAVHVPLTLE AQLEA RALM MSTNNILSPA NGEPIIVPSQ DVVLGLYYMT RDCVNAKGEG MVLTGPKEAE RLYRSGLASL HARVKVRITE YEKDAN GEL VAKTSLKDTT VGRAILWMIV PKGLPYSIVN QALGKKAISK MLNTCYRILG LKPTVIFADQ IMYTGFAYAA RSGASVG ID DMVIPEKKHE IISEAEAEVA EIQEQFQSGL VTAGERYNKV IDIWAAANDR VSKAMMDNLQ TETVINRDGQ EEKQVSFN S IYMMADSGAR GSAAQIRQLA GMRGLMAKPD GSIIETPITA NFREGLNVLQ YFISTHGARK GLADTALKTA NSGYLTRRL VDVAQDLVVT EDDCGTHEGI MMTPVIEGGD VKEPLRDRVL GRVTAEDVLK PGTADILVPR NTLLHEQWCD LLEENSVDAV KVRSVVSCD TDFGVCAHCY GRDLARGHII NKGEAIGVIA AQSIGEPGTQ LTMRTFHIGG AASRAAAESS IQVKNKGSIK L SNVKSVVN SSGKLVITSR NTELKLIDEF GRTKESYKVP YGAVLAKGDG EQVAGGETVA NWDPHTMPVI TEVSGFVRFT DM IDGQTIT RQTDELTGLS SLVVLDSAER TAGGKDLRPA LKIVDAQGND VLIPGTDMPA QYFLPGKAIV QLEDGVQISS GDT LARIPQ ESGGTKDITG GLPRVADLFE ARRPKEPAIL AEISGIVSFG KETKGKRRLV ITPVDGSDPY EEMIPKWRQL NVFE GERVE RGDVISDGPE APHDILRLRG VHAVTRYIVN EVQDVYRLQG VKINDKHIEV IVRQMLRKAT IVNAGSSDFL EGEQV EYSR VKIANRELEA NGKVGATYSR DLLGITKASL ATESFISAAS FQETTRVLTE AAVAGKRDEL RGLKENVIVG RLIPAG TGY AYHQDRMRRR AAGEAPAAPQ VTAEDASASL AELLNAGLGG SDNELERRAS ENLYFQGHHH HHHHHHH

UniProtKB: DNA-directed RNA polymerase subunit beta'

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Macromolecule #6: DNA-directed RNA polymerase subunit omega

MacromoleculeName: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 10.249547 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARVTVQDAV EKIGNRFDLV LVAARRARQM QVGGKDPLVP EENDKTTVIA LREIEEGLIN NQILDVRERQ EQQEQEAAEL QAVTAIAEG RR

UniProtKB: DNA-directed RNA polymerase subunit omega

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Macromolecule #7: RNA polymerase sigma factor RpoD

MacromoleculeName: RNA polymerase sigma factor RpoD / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 71.842812 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGHMEQNPQ SQLKLLVTRG KEQGYLTYAE VNDHLPEDIV DSDQIEDIIQ MINDMGIQVM EEAPDADDLM LAENTADED AAEAAAQVLS SVESEIGRTT DPVRMYMREM GTVELLTREG EIDIAKRIED GINQVQCSVA EYPEAITYLL E QYDRVEAE ...String:
MGSSHHHHHH SSGHMEQNPQ SQLKLLVTRG KEQGYLTYAE VNDHLPEDIV DSDQIEDIIQ MINDMGIQVM EEAPDADDLM LAENTADED AAEAAAQVLS SVESEIGRTT DPVRMYMREM GTVELLTREG EIDIAKRIED GINQVQCSVA EYPEAITYLL E QYDRVEAE EARLSDLITG FVDPNAEEDL APTATHVGSE LSQEDLDDDE DEDEEDGDDD SADDDNSIDP ELAREKFAEL RA QYVVTRD TIKAKGRSHA TAQEEILKLS EVFKQFRLVP KQFDYLVNSM RVMMDRVRTQ ERLIMKLCVE QCKMPKKNFI TLF TGNETS DTWFNAAIAM NKPWSEKLHD VSEEVHRALQ KLQQIEEETG LTIEQVKDIN RRMSIGEAKA RRAKKEMVEA NLRL VISIA KKYTNRGLQF LDLIQEGNIG LMKAVDKFEY RRGYKFSTYA TWWIRQAITR SIADQARTIR IPVHMIETIN KLNRI SRQM LQEMGREPTP EELAERMLMP EDKIRKVLKI AKEPISMETP IGDDEDSHLG DFIEDTTLEL PLDSATTESL CAATHD VLA GLTAREAKVL RMRFGIDMNT DYTLEEVGKQ FDVTRERIRQ IEAKALRKLR HPSRSEVPRS FLDD

UniProtKB: RNA polymerase sigma factor RpoD

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Macromolecule #8: Q protein

MacromoleculeName: Q protein / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Phage 21 (virus)
Molecular weightTheoretical: 18.668789 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGIRELNLTK EQHEWLNGWL ELWGAWVYSG RLEKRMSSVI AKFMESVEPG RVMTRPMCND DDGMLISQVV DSVMYIDKKA FGILLSYYA HGSSKHAIAS YYHRVARPRK MLCRGGGRIQ KPSLATCRRE VDEILNASLF MIYPVLDSAF KNRKRVEKIK H VA

UniProtKB: Q protein

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Macromolecule #9: RNA (5'-R(P*UP*GP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')

MacromoleculeName: RNA (5'-R(P*UP*GP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3') / type: rna / ID: 9 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 3.626226 KDa
SequenceString:
UGGGAGAGGU A

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Macromolecule #10: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 10 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #11: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 11 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration9 mg/mL
BufferpH: 7.8
Component:
ConcentrationName
10.0 mMTris-HCl
100.0 mMsodium chloride
1.0 mMMagnesium chloride
1.0 mMdithiothreitol
8.0 mMChapso
GridModel: UltrAuFoil / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 300 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Number real images: 3010 / Average electron dose: 1.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 47608 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1045380
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5ipl


Details: 5MEY, 4YLN
Final reconstructionNumber classes used: 5 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 150310
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 8 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5ipl

chain_id: A, source_name: PDB, initial_model_type: experimental model

5ipl

chain_id: B, source_name: PDB, initial_model_type: experimental model

5ipl

chain_id: C, source_name: PDB, initial_model_type: experimental model

5ipl

chain_id: D, source_name: PDB, initial_model_type: experimental model

5ipl

chain_id: E, source_name: PDB, initial_model_type: experimental model

4mey

chain_id: F, source_name: PDB, initial_model_type: experimental model

4yln

chain_id: 1, source_name: PDB, initial_model_type: experimental model

4yln

chain_id: 2, source_name: PDB, initial_model_type: experimental model

4yln

chain_id: 3, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 50 / Target criteria: 0.143
Output model

PDB-6p18:
Q21 transcription antitermination complex: loading complex

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